PROJECT SUMMARY Orofacial clefts (OFCs) are the most common craniofacial birth defect in humans and are caused by multiple genetic and environmental risk factors. Elucidating the etiology of OFCs is critical not only for our knowledge of developmental biology and for how clefts arise, but ultimately for improved prevention, treatment, and prognosis for individuals affected by OFCs. Clinical applications of exome or genome sequencing are growing, but the usability for OFCs is hindered by the missing fraction of heritable risk and a poor understanding of phenotypic heterogeneity and variable expression of genetic factors. The goal of the current proposal is to determine the rare variant contribution to the genetic architecture of OFCs and its substantial phenotypic heterogeneity. The data come from the Gabriella Miller Kids First Pediatric Research Program, which provided whole genome sequencing (WGS) of 979 trios with OFCs. We will perform a comprehensive analysis of de novo and rare inherited coding variation and evaluate rare variants as modifiers of OFC severity. Finally, we will combine WGS data with targeted sequence data for the IRF6 locus, which contains multiple independent signals and phenotypic modifiers, to perform a detailed phenotype-based fine mapping analysis. These analyses will provide further insight into the genetic architecture of OFCs and will reveal the full potential of WGS data for OFCs.